A Spirit Airlines Inc. Airbus A320-232 jet prepares to take off at Ronald Reagan National Airport in Arlington, Virginia, U.S., on Friday, Aug. 26, 2011. The partial shutdown of the U.S. FAA last month could cost taxpayers at least $468 million. The money includes taxes on airline tickets and aviation fuel that the government could not collect during the 16 days while Congress deadlocked over legislation to keep the FAA fully operating. Photographer: Andrew Harrer/Bloomberg

Photo: Andrew Harrer, Bloomberg

A Spirit Airlines Inc. Airbus A320-232 jet prepares to take off at...

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Southwest Airlines received the least complaints per 100,000 passengers.

Photo: Joyce Marshall, McClatchy-Tribune News Service

Southwest Airlines received the least complaints per 100,000...

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Ben Baldanza, president and CEO of Spirit, defends the airline as offering people a cheaper option.

Photo: Andrew Harrer, Bloomberg

Ben Baldanza, president and CEO of Spirit, defends the airline as...

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Frontier Airlines received the second most complaints.

Photo: Damian Dovarganes

Frontier Airlines received the second most complaints.

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United Airlines was the third most-complained about airline...

Photo: Nam Y. Huh, Associated Press

United Airlines was the third most-complained about airline...

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...followed by American Airlines.

Photo: LM Otero, Associated Press

...followed by American Airlines.

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Along with Southwest, Alaska Airlines also generated relatively few complaints for their size...

Photo: Ted S. Warren, Associated Press

Along with Southwest, Alaska Airlines also generated relatively few...

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Spirit Airlines passenger, Brian Svigel, left, and Brian McClain, second from left, get instructions from a Spirit Airlines employee demonstrating the airlines carry-on baggage template, two sizes, the free smaller size for a "personal item" and the larger size that the airline charges $40 for a carry-on before their flight to Las Vegas at Denver International Airport Thursday morning. Both of their bags, which they thought would qualify as "carry-on" bags did not fit and both had to pay the fee.

Photo: ANDY CROSS, DP

Spirit Airlines passenger, Brian Svigel, left, and Brian McClain,...

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Spirit is making money and its stock is flying high. Its shares are up
about 136 percent over the past year, compared with an 87 percent gain
for Southwest stock.

Photo: Joe Raedle, Getty Images

Spirit is making money and its stock is flying high. Its shares are...

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In this file photo Spirit Airlines CEO Ben Baldanza speaks, listens and reacts during an interview on in New York.

Spirit Airlines generated the most complaints per 100,000 passengers and Southwest Airlines the least, according to a study released Thursday.

The study, by the CalPIRG Education Fund, analyzed complaint data for 13 large domestic airlines lodged with the U.S. Department of Transportation's Aviation Consumer Protection Division from 2009 through 2013. It found that most complaints were about delayed or canceled flights.

Spirit, known for ultra-low fares and pesky fees, generated the most complaints for an airline of its size by a wide margin. "Each year, Spirit's passengers were about three times as likely to file a complaint as the second-place airline, and its complaints volume is trending upward over time," the report said.

"They are notorious for nickel-and-diming passengers," said Austin Price, CalPIRG field director.

Spirit charges $26 to $100 to carry on a bag, $1 to $50 to choose a seat and $10 to get a boarding pass printed at the airport, according to the airline's website.

Spirit said in an e-mail that "many of the (Department of Transportation) complaints about Spirit are driven by our customers not fully understanding that we offer unbundled fares that let them control how much they spend. In 2013, we had a total of 1,021 ... complaints and served over 12 million customers. While we want every customer to have a great experience, eight complaints per 100,000 enplanements is a pretty small number." (Every time a passenger boards a plane it counts as one enplanement.) It added that it is "working every day to reduce complaints."

CalPIRG's numbers for 2013, based on an early estimate, were slightly different for Spirit and worked out to 9.4 complaints per enplanement. Laura Murray, the report's author, said her numbers might be "a little off, but it doesn't change the fact that they're still in first place by a mile."

After Spirit, the carriers that ranked highest on the complaint scale were Frontier Airlines, United Airlines, and American Airlines.

Southwest generated the fewest complaints per 100,000 passengers in each of the past five years. Alaska Airlines, AirTran Airways and JetBlue Airlines also generated relatively few complaints for their size.

Even when things go wrong, Southwest customers seem not to complain to the Transportation Department as much as other airline passengers.

For example, Southwest ranked in the middle of the pack when it came to mishandling bags in 2013, yet it had the fewest baggage complaints per 100,000 passengers registered with the federal agency.

Because it is one of the few airlines that let all passengers check bags for free, perhaps "they don't complain as much about lost bags," says George Hobica, founder of the AirfareWatchdog website.

Another anomaly: Southwest's on-time performance ranked in the bottom half of airlines in 2013, and it had the worst record when it came to flight delays under the airline's control. Yet it had the fewest complaints per 100,000 passengers about flight problems such as delays and cancellations.

"Their customers aren't complaining" to the Department of Transportation, Murray said. "Maybe they are addressing it at the airport, or their customer service is much more effective" than other airlines.

Hobica says Southwest's on-time performance has suffered as it has expanded from out-of-the-way airports to larger, delay-prone ones in cities such as New York and Atlanta. But it wards off complaints with "jolly" employees and customer-friendly policies. "They give you a credit if you cancel or change your reservation versus the $200 fee that American, Delta and United charge to change" a nonrefundable ticket.

The CalPIRG study included airlines that had 10 million or more enplanements (flight segments) in 2013, Murray said. Popular airlines such as Virgin America, based in Burlingame, and Hawaiian Airlines missed the cutoff.

Despite its horrendous complaint record, Spirit is making money and its stock is flying high. Its shares are up about 136 percent over the past year, compared with an 87 percent gain for Southwest stock.

Even with all the fees, "Spirit is still cheaper" in many cases. And for some people, that's all that matters, Hobica said. "Their CEO is famous for saying, basically, you get what you pay for."